The first is creating new documents: Lisa's attempt was understandable, Windows' File/New menu tends to miss out all non-Microsoft file types. Sometimes you just need to open the app, like inkscape, to get started off.
The second problem is with things inherently app-based like games. Sure, one could have 'File/New/Factorio game' in the Explorer menu (although that just copies a template file, it doesn't allow for customization) and one could make it so that double-clicking a save game opens Factorio (assuming .fac or something is associated with the correct program), but the usual way is start -> steam -> factorio -> load game (or, more likely, 'continue game' which the document-based approach also can't handle well).
I like my documents and my music organized into folders, most of the time I'm not fussed where my savegames are stored (steam cloud backups, after all). A sensibly done hybrid approach is best.
How to organize my Factorio blueprints is another question ...